[gmx-users] All-atom MD simulation of a protein at 323K and 283K

Erik Marklund erik.marklund at chem.ox.ac.uk
Thu May 8 11:40:13 CEST 2014


What you need to be aware of is that heat capacities aren't well reflected by the force field, hence the temperature offset from 300 K may not be well reflected either. As such, your simulation at 323 K may in fact be more representative of let's say 335 K or something. I can't comment on the magnitude of this effect however.

Erik Marklund

On 8 May 2014, at 07:48, Pappu Kumar <papuu_k at yahoo.com> wrote:

> I am trying to compare the stability of a protein from two organisms which live in the aforesaid temperature. I am wondering it would make sense to run MD simulation in gromacs with Amber99sb in these temperature since force field parameterization was carried out in room temperature. 
> I am also thinking about running simulated annealing from 323K to 283K in order to compare the stability of the two proteins. Thank you.
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